This paper presents a list of species of rotifers and lower crustaceans from water bodies adjacent to Lake Baikal and streams of Baikalo-Lensky State Reserve (B-LSR) and Baikal Biosphere Reserve (BBR). 130 zooplankton species have been registered in B-LSR small lakes. Such an abundance is attributed to a variety of ecological and biotopical conditions and immediate proximity to Lake Baikal. Zooplankton of BBR is represented by 87 species, many of which are indicators of acid waters as the majority of water bodies are marsh lakes.